Linear chemically sensitive electron tomography using DualEELS and dictionary-based compressed sensing

We have investigated the use of DualEELS in elementally sensitive tilt series tomography in the scanning transmission electron microscope. A procedure is implemented using deconvolution to remove the effects of multiple scattering, followed by normalisation by the zero loss peak intensity. This is performed to produce a signal that is linearly dependent on the projected density of the element in each pixel. This method is compared with one that does not include deconvolution (although normalisation by the zero loss peak intensity is still performed). Additionaly, we compare the 3D reconstruction using a new compressed sensing algorithm, DLET, with the well-established SIRT algorithm. VC precipitates, which are extracted from a steel on a carbon replica, are used in this study. It is found that the use of this linear signal results in a very even density throughout the precipitates. However, when deconvolution is omitted, a slight density reduction is observed in the cores of the precipitates (a so-called cupping artefact). Additionally, it is clearly demonstrated that the 3D morphology is much better reproduced using the DLET algorithm, with very little elongation in the missing wedge direction. It is therefore concluded that reliable elementally sensitive tilt tomography using EELS requires the appropriate use of DualEELS together with a suitable reconstruction algorithm, such as the compressed sensing based reconstruction algorithm used here, to make the best use of the limited data volume and signal to noise inherent in core-loss EELS

Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies

A data-driven approach for predicting printability in metal additive manufacturing processes

Metal powder-bed fusion additive manufacturing technologies offer numerous benefits to the manufacturing industry. However, the current approach to printability analysis, determining which components are likely to build unsuccessfully, prior to manufacture, is based on ad-hoc rules and engineering experience. Consequently, to allow full exploitation of the benefits of additive manufacturing, there is a demand for a fully systematic approach to the problem. In this paper we focus on the impact of geometry in printability analysis. For the first time, we detail a machine learning framework for determining the geometric limits of printability in additive manufacturing processes. This framework consists of three main components. First, we detail how to construct strenuous test artefacts capable of pushing an additive manufacturing process to its limits. Secondly, we explain how to measure the printability of an additively manufactured test artefact. Finally, we construct a predictive model capable of estimating the printability of a given artefact before it is additively manufactured. We test all steps of our framework, and show that our predictive model approaches an estimate of the maximum performance obtainable due to inherent stochasticity in the underlying additive manufacturing process. © 2020, The Author(s)

Representational organization of novel task sets during proactive encoding

Recent multivariate analyses of brain data have boosted our understanding of the organizational principles that shape neural coding. However, most of this progress has focused on perceptual visual regions (Connolly et al., 2012), whereas far less is known about the organization of more abstract, action-oriented representations. In this study, we focused on humans{\textquoteright} remarkable ability to turn novel instructions into actions. While previous research shows that instruction encoding is tightly linked to proactive activations in fronto-parietal brain regions, little is known about the structure that orchestrates such anticipatory representation. We collected fMRI data while participants (both males and females) followed novel complex verbal rules that varied across control-related variables (integrating within/across stimuli dimensions, response complexity, target category) and reward expectations. Using Representational Similarity Analysis (Kriegeskorte et al., 2008) we explored where in the brain these variables explained the organization of novel task encoding, and whether motivation modulated these representational spaces. Instruction representations in the lateral prefrontal cortex were structured by the three control-related variables, while intraparietal sulcus encoded response complexity and the fusiform gyrus and precuneus organized its activity according to the relevant stimulus category. Reward exerted a general effect, increasing the representational similarity among different instructions, which was robustly correlated with behavioral improvements. Overall, our results highlight the flexibility of proactive task encoding, governed by distinct representational organizations in specific brain regions. They also stress the variability of motivation-control interactions, which appear to be highly dependent on task attributes such as complexity or novelty.SIGNIFICANCE STATEMENTIn comparison with other primates, humans display a remarkable success in novel task contexts thanks to our ability to transform instructions into effective actions. This skill is associated with proactive task-set reconfigurations in fronto-parietal cortices. It remains yet unknown, however, how the brain encodes in anticipation the flexible, rich repertoire of novel tasks that we can achieve. Here we explored cognitive control and motivation-related variables that might orchestrate the representational space for novel instructions. Our results showed that different dimensions become relevant for task prospective encoding depending on the brain region, and that the lateral prefrontal cortex simultaneously organized task representations following different control-related variables. Motivation exerted a general modulation upon this process, diminishing rather than increasing distances among instruction representations

3D Multi-Scale Behavior of Granular Materials using Experimental and Numerical Techniques

Constitutive modeling of granular material behavior has generally been based on global response of laboratory-size specimens or larger models with little understanding of the fundamental mechanics that drive the global response. Many studies have acknowledged the importance of micro-scale and meso-scale mechanics on the constitutive behavior of granular materials. However, much knowledge is still missing to develop and improve robust micromechanical constitutive models. The research in this dissertation contributes to this knowledge gap for many potential applications using novel experimental techniques to investigate the three-dimensional (3D) behavior of granular materials. Critical micromechanics measurements at multiple scales are investigated by combining 3D synchrotron micro-computed tomography (SMT), 3D image analysis, and finite element analysis (FEA). At the single particle level (micro-scale), particle fracture was examined at strain rates of 0.2 mm/min and 2 m/s using quasi-static unconfined compression, unconfined mini-Kolsky bar, and x-ray imaging techniques. Surface reconstructions of particles were generated and exported to Abaqus FEA software, where quasi-static and higher rate loading curves and crack propagation were simulated with good accuracy. Stress concentrations in oddly shaped particles during FEA simulations resulted in more realistic fracture stresses than theoretical models. A nonlinear multivariable statistical model was developed to predict force required to fracture individual particles with known internal structure and loading geometry. At the meso-scale, 3D SMT imaging during in-situ triaxial testing of granular materials were used to identify particle morphology, contacts, kinematics and interparticle behavior. Micro shear bands (MSB) were exposed during pre-peak stress using a new relative particle displacement concept developed in this dissertation. MSB for spherical particles (glass beads) had larger thickness (3d50 to 5d50) than that of angular sands (such as F35 Ottawa sand, MSB thickness of 1d50 to 3d50). Particle morphology also plays a significant role in the onset and growth of shear bands and global fabric evolution of granular materials. More spherical particles typically exhibit more homogeneous internal anisotropy. Fabric of particles within the shear band (at higher densities and confining pressures) exhibits a peak and decrease into steady-state. Also, experimental fabric produces more accurate strength and deformation predictions in constitutive models that incorporate fabric evolution

Volumetric cloud generation using a Chinese brush calligraphy style

Includes bibliographical references.Clouds are an important feature of any real or simulated environment in which the sky is visible. Their amorphous, ever-changing and illuminated features make the sky vivid and beautiful. However, these features increase both the complexity of real time rendering and modelling. It is difficult to design and build volumetric clouds in an easy and intuitive way, particularly if the interface is intended for artists rather than programmers. We propose a novel modelling system motivated by an ancient painting style, Chinese Landscape Painting, to address this problem. With the use of only one brush and one colour, an artist can paint a vivid and detailed landscape efficiently. In this research, we develop three emulations of a Chinese brush: a skeleton-based brush, a 2D texture footprint and a dynamic 3D footprint, all driven by the motion and pressure of a stylus pen. We propose a hybrid mapping to generate both the body and surface of volumetric clouds from the brush footprints. Our interface integrates these components along with 3D canvas control and GPU-based volumetric rendering into an interactive cloud modelling system. Our cloud modelling system is able to create various types of clouds occurring in nature. User tests indicate that our brush calligraphy approach is preferred to conventional volumetric cloud modelling and that it produces convincing 3D cloud formations in an intuitive and interactive fashion. While traditional modelling systems focus on surface generation of 3D objects, our brush calligraphy technique constructs the interior structure. This forms the basis of a new modelling style for objects with amorphous shape

Visual Exploration And Information Analytics Of High-Dimensional Medical Images

Data visualization has transformed how we analyze increasingly large and complex data sets. Advanced visual tools logically represent data in a way that communicates the most important information inherent within it and culminate the analysis with an insightful conclusion. Automated analysis disciplines - such as data mining, machine learning, and statistics - have traditionally been the most dominant fields for data analysis. It has been complemented with a near-ubiquitous adoption of specialized hardware and software environments that handle the storage, retrieval, and pre- and postprocessing of digital data. The addition of interactive visualization tools allows an active human participant in the model creation process. The advantage is a data-driven approach where the constraints and assumptions of the model can be explored and chosen based on human insight and confirmed on demand by the analytic system. This translates to a better understanding of data and a more effective knowledge discovery. This trend has become very popular across various domains, not limited to machine learning, simulation, computer vision, genetics, stock market, data mining, and geography. In this dissertation, we highlight the role of visualization within the context of medical image analysis in the field of neuroimaging. The analysis of brain images has uncovered amazing traits about its underlying dynamics. Multiple image modalities capture qualitatively different internal brain mechanisms and abstract it within the information space of that modality. Computational studies based on these modalities help correlate the high-level brain function measurements with abnormal human behavior. These functional maps are easily projected in the physical space through accurate 3-D brain reconstructions and visualized in excellent detail from different anatomical vantage points. Statistical models built for comparative analysis across subject groups test for significant variance within the features and localize abnormal behaviors contextualizing the high-level brain activity. Currently, the task of identifying the features is based on empirical evidence, and preparing data for testing is time-consuming. Correlations among features are usually ignored due to lack of insight. With a multitude of features available and with new emerging modalities appearing, the process of identifying the salient features and their interdependencies becomes more difficult to perceive. This limits the analysis only to certain discernible features, thus limiting human judgments regarding the most important process that governs the symptom and hinders prediction. These shortcomings can be addressed using an analytical system that leverages data-driven techniques for guiding the user toward discovering relevant hypotheses. The research contributions within this dissertation encompass multidisciplinary fields of study not limited to geometry processing, computer vision, and 3-D visualization. However, the principal achievement of this research is the design and development of an interactive system for multimodality integration of medical images. The research proceeds in various stages, which are important to reach the desired goal. The different stages are briefly described as follows: First, we develop a rigorous geometry computation framework for brain surface matching. The brain is a highly convoluted structure of closed topology. Surface parameterization explicitly captures the non-Euclidean geometry of the cortical surface and helps derive a more accurate registration of brain surfaces. We describe a technique based on conformal parameterization that creates a bijective mapping to the canonical domain, where surface operations can be performed with improved efficiency and feasibility. Subdividing the brain into a finite set of anatomical elements provides the structural basis for a categorical division of anatomical view points and a spatial context for statistical analysis. We present statistically significant results of our analysis into functional and morphological features for a variety of brain disorders. Second, we design and develop an intelligent and interactive system for visual analysis of brain disorders by utilizing the complete feature space across all modalities. Each subdivided anatomical unit is specialized by a vector of features that overlap within that element. The analytical framework provides the necessary interactivity for exploration of salient features and discovering relevant hypotheses. It provides visualization tools for confirming model results and an easy-to-use interface for manipulating parameters for feature selection and filtering. It provides coordinated display views for visualizing multiple features across multiple subject groups, visual representations for highlighting interdependencies and correlations between features, and an efficient data-management solution for maintaining provenance and issuing formal data queries to the back end